{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Analysis of Acetonitrile to calculate the dielectric constant\n",
    "\n",
    "Assumes the path to PyLAT/src has been added to PYTHONPATH"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Import Classes\n",
    "\n",
    "import and initialize required classes for calculations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from calcDielectricConstant import calcDielectricConstant\n",
    "from getAtomCharges import getatomcharges\n",
    "from getCoordinationNumber import getcoordinationnumber\n",
    "\n",
    "dec=calcDielectricConstant()\n",
    "gc=getatomcharges()\n",
    "gcn=getcoordinationnumber()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Define input \n",
    "input for dielectric constant calculations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "datfilename='mol.data'\n",
    "trjfilename=['mol.lammpstrj']\n",
    "temp=298\n",
    "verb=0\n",
    "DEC_start=0\n",
    "output={}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Preliminary Calculations\n",
    "Preliminary calculations for DEC calculation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "n=gc.findnumatoms(datfilename)\n",
    "(molcharges,atomcharges,n)=gc.getmolcharges(datfilename,n)\n",
    "(V,Lx,Ly,Lz)=gcn.getvolume(trjfilename[0])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Property Calculations\n",
    "Calculation of dielectric constant"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "output = dec.calcDEC(atomcharges,trjfilename,temp,output,V,verb,DEC_start)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot dielectric constant"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "23.2845053628\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fe54632f510>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib inline\n",
    "from matplotlib import pyplot as plt\n",
    "\n",
    "DEC=output['Dielectric Constant']['list']\n",
    "count = range(0,len(DEC))\n",
    "\n",
    "plt.xlabel('Timesteps')\n",
    "plt.ylabel(r'$\\epsilon$')\n",
    "plt.plot(count,DEC)\n",
    "\n",
    "print(DEC[-1])"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.14"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}
